I just want to get a second opinion before I go the route I think I need to take.

Bit of background:

I have my cousin's desktop here that I'm working on. A few weeks ago while I was in the middle of doing a Windows Update, the PSU blew, literally. I suspect the PSU was flaky anyway. So it popped and I went and got him a nice new one. I put it in, but the machine was still acting a bit flaky. He was using an extremely low profile video card (I think it was a GeForce 210) and has an HDMI splitter running off the machine. It kept hanging after the monitors/TVs would go to sleep. Sometimes while watching videos after a few minutes the entire machine would just turn off. I did some digging and the temps were all fine, there weren't any errors in any of the logs, it just kept acting wonky. So I said, bite the bullet and get a better card. He doesn't game at all and mostly just browses from the TV in the garage so I figured a newer low profile would be fine. Picked up an evga GT 640. I put it in the machine and had nVidia clean out the old drivers and do a clean install. It seemed to go perfect until nVidia Experience said there were newer drivers. I let it do it's thing but it failed on the driver install.

I did some more digging and found this wasn't uncommon lately but nothing I tried forced the drivers to install. Ultimately, I opted to reinstall Windows. I reinstalled Windows 7 64-bit, downloaded the latest nVidia drivers and low and behold, they failed to install. There was one abnormality I did notice that I couldn't resolve even with a fresh reinstall of Windows. The integrated graphics kept showing up under Display Adapters in the Device Manager. Thing is, nothing is/was plugged into the motherboard's VGA spot at all. The bios is set to PCIe as the default video but it just won't go away. At this point I was wondering if the new video card was borked so I took it out and put it into my HTPC (which has an AMD CPU with integrated GPU on the chip). As soon as Windows came up, I went into the device manager and it shows only the GT 640.

Is the motherboard pooched in my cousin's desktop? I'm beginning to think it is. Maybe when the PSU went it caused some damage to the motherboard?

That is all possible, yes. Anything connected to your PSU is potentially endangered and can be borked by it. Does he have onboard video, at all?

Yes he does. It's actually an nVidia 630a (If my memory is correct) onboard. But because he uses HDMI, we never touched it as the motherboard only had a VGA port. So the displays have always been connected through HDMI.

Before I reinstalled Windows, I even went so far as the pull the CMOS battery in an attempt to force the machine to recognize the 640 and disable the onboard on it's own, but that never happened. It still showed the onboard as well as the 640 (however the 640 always showed as Standard VGA Adapter) cause I couldn't install the nVidia drivers. Actually, if I let Windows Update install the drivers (which is what happened the first time), it installed an old version of the nVidia drivers, but showed both GPU's and wouldn't let me update them either. It's been driving me insane because there's no reason the onboard should be there with the dedicated card in.